It's a very minor issue, I would be fine with letting it appear on start.

Some more things about the GUI on XP.
You can't interact with the title bar at all. Hover on the X button isn't even working.
Also the area around it doesn't seem to redraw correctly, this is how it looks like if you drag a window over it:

I just noticed that the popup plugin is wrongly shown now when clicking on the prev/next buttons in the GUI, even though the plugin preferences is set to "User interaction without main UI". If you press Ctrl-arrow though, it's correctly not showing up.

Tuniac can now tell plugins these things about why a song changed:
-auto song change with focus
-auto song change without focus
-manual song change with focus
-manual song change without focus

Popup notify now has these options"
-always (all)
-always when no focus (auto and manual without focus)
-Auto song changes (auto with and without focus)
-Auto song changes no focus (auto without focus)

I would now say "Always when no focus" suits what you want.

Also because it was annoying me, double clicking plugins in the prefs window will now open its settings windows, if it has one..

And here I'll come again to complicate it
Now the option I wanted is actually gone. What I wanted was that it should show only on blind manual changes. Like how it worked before except it doesn't need to show when interacting with the GUI.
Personally I think it's much more useful with having it only on manual changes than only on automatic. Having it all the time is a bit distracting I think, it's when I actually want to change song that I want to see which song I'm changing to.
So what I propose from your newest changes is to replace the options "automatic song changes" to a only manual change.